SARS-CoV-2 Lineage Variant Summary

Nucleotide variants related to lineages of concern are indicated in yellow above a schematic SARS-CoV-2 genome. Primer pairs that do not overlap with variants associated with these lineages are shown in green. Pairs that do overlap are indicated in orange. Affected primers:

N Gene Variants

S Gene Variants

Orf1 Gene (16.5kb) Variants


Sequences reported in Sequence Sources for each lineage were aligned to the NC_045512.2 reference sequence (minimap2). Variants > 20% frequency (freebayes) were evaluated for overlap with primer regions (bedtools) and displayed (Geneious Prime 2021.0.3).

Sequence Sources:

Virological. “Preliminary Genomic Characterisation of an Emergent SARS-CoV-2 Lineage in the UK Defined by a Novel Set of Spike Mutations - SARS-CoV-2 Coronavirus / NCoV-2019 Genomic Epidemiology,” December 18, 2020. .

Virological. “SARS-CoV-2 Reinfection by the New Variant of Concern (VOC) P.1 in Amazonas, Brazil - SARS-CoV-2 Coronavirus / NCoV-2019 Genomic Epidemiology,” January 18, 2021. .

Tegally, Houriiyah, Eduan Wilkinson, Marta Giovanetti, Arash Iranzadeh, Vagner Fonseca, Jennifer Giandhari, Deelan Doolabh, et al. “Emergence and Rapid Spread of a New Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2) Lineage with Multiple Spike Mutations in South Africa.” MedRxiv, December 22, 2020, 2020.12.21.20248640. .

Zhang, Wenjuan, Brian D. Davis, Stephanie S. Chen, Jorge M. Sincuir Martinez, Jasmine T. Plummer, and Eric Vail. “Emergence of a Novel SARS-CoV-2 Strain in Southern California, USA.” MedRxiv, January 20, 2021, 2021.01.18.21249786. .

West, Anthony P., Christopher O. Barnes, Zhi Yang, and Pamela J. Bjorkman. “SARS-CoV-2 Lineage B.1.526 Emerging in the New York Region Detected by Software Utility Created to Query the Spike Mutational Landscape.” BioRxiv, February 23, 2021, 2021.02.14.431043. .


Li, Heng. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34, no. 18 (September 15, 2018): 3094–3100. .

Garrison, Erik, and Gabor Marth. “Haplotype-Based Variant Detection from Short-Read Sequencing.” ArXiv:1207.3907 [q-Bio], July 20, 2012.

Quinlan, Aaron R, and Ira M Hall. “BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features.” Bioinformatics (Oxford, England) 26 (2010): 841–42. .